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Lon protease proteolytic domain

Analyse Lon protease proteolytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WYS
Type: protein
Length: 570 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease homolog, mitochondrial
EC: 3.4.21.53
UniProt: P36776
Ligands: SO4
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	189	36% helix, 26% strand	P36776
B	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	191	36% helix, 26% strand	P36776
C	Lon protease homolog, mitochondrial (EC 3.4.21.53)	protein	190	37% helix, 25% strand	P36776

Ligands and binding sites

SO4 · Sulfate ion · ion · 5 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	912	0.76	0.79	78	empty
2	76	0.60	0.89	23	empty
3	262	0.58	0.78	31	empty
4	90	0.39	0.77	24	SO4
5	84	0.37	0.76	25	SO4

Interfaces

3 interfaces between chains.

A–B · 880 Å² buried · 14 hydrogen bonds · protein-protein
B–C · 635 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 485 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

6WYS · Lon protease proteolytic domain · the same entry in another collection · chain A against A, TM-score 1.00
P36776 · AlphaFold monomer V2.0 prediction for lon protease homolog, mitochondrial (P36776) · a predicted model of the same protein · chain A against A, TM-score 0.98

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P36776
Elsewhere: RCSB PDB 6WYS · PDBe 6WYS · UniProt P36776

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